I agree with this completely. In a sense, the dystopian presentation of a movie like Blade Runner or Akira feels oddly more comforting. Street venders, gangs of kids doing nothing in particular, smokers, etc. Even the cleanest, most polite scandinavian social democracy still has all these things, but they're conveniently left out of these "utopian" visions.
I think, if anything triggers our discomfort, it's the subconscious question of what happened to them.
I feel the same way about sterile utopia vs. messy blade runner-type worlds.
Interestingly I'm reading Snow Crash right now, which takes place in a world that is arguable similar to the one in Blade Runner, but the anarcho-capitalist aspect of the America depicted just really gives me the creeps.
I think, if anything triggers our discomfort, it's the subconscious question of what happened to them.